Inflammation is a well-known mechanism associated with organic gastrointestinal (GI) disorders, such as the Inflammatory Bowel Disease. However, only recently has evidence emerged that an underlying inflammatory mechanism may be associated with the previously termed functional gastrointestinal disorders associated with chronic GI symptoms such as diarrhea and chronic abdominal pain (CAP) with no identified organic cause. In our studies, we found evidence for differential levels of specific candidate biomarkers in GI biopsies from patients with histologically defined inflammatory phenotypes. The IL-6 levels in the colonic biopsies from pediatric patients with inflammatory phenotypes were found to be significantly increased compared to controls with non-inflammatory phenotypes (Henderson, et al., 2012, WJGP). In the same colonic biopsies, the number of mast cells was significantly higher in patients with no evidence of histological inflammation compared to patients with inflammatory phenotype. Interestingly, no difference in IL-6 and mast cell staining was observed in the upper GI tract biopsies, suggesting significance of the colonic environment in chronic GI symptom pathology. Such significance was corroborated by our results using an intestinal permeability test solution, ingested by participants following an overnight fast. The test solution contains four sugar probes absorbable at various sites along the GI tract. Five hours after ingestion, excreted urine analysis of the four sugar probes and raffinose (an internal standard) was performed using mass spectrometry method. Based on these analyses, we showed that patients with CAP, meeting Rome III criteria for Irritable Bowel Syndrome (IBS), had a significantly decreased colonic permeability, represented by differential urinary sucralose output, compared to controls with no IBS. Of the IBS patients, 55% had diarrhea. Changes in sucrose urine output, representing gastric permeability, and changes in lactulose-to-mannitol ratio, representing small intestinal permeability, were not observed (Del Valle-Pinero, et al., 2013). This unexpected finding, which points to altered colonic permeability as one of the likely mechanisms for the observed GI aberrations in patient with chronic GI symptoms, together with our histological evidence from the colonic biopsies, serve as a starting point for a closer investigation into candidate cellular and molecular players within the pathways and microenvironment contributing to chronic GI symptoms. Our preliminary investigation of such molecular players recently revealed mRNA and microRNA (miR) signatures associated with carefully phenotyped patients having chronic GI symptoms. In IBS patients, we found elevated levels of two circulating miRs, the hsa-miR-342-3p and hsa-miR-150, compared to controls with similar age, BMI, and ethnicity (Fourie, et al., 2014). Within the IBS group, IBS-constipation patients but not the IBS-diarrhea patients had elevated hsa-miR-342-3p level compared to controls. The involvement of inflammation is suggested by these specific miRs, which are linked to inflammation in other diseases, e.g., cancer. Gender-specific microRNA signatures were further found in a subset of patients with Non-alcoholic Fatty Liver Disease (NAFLD). Male NAFLD patients had significantly upregulated expressions of the hsa-miR-432-5p, hsa-miR-578 and hsa-miR-155-5p compared to female NAFLD patients. The hsa-miR-432-5p and hsa-miR-301b levels were significantly higher in NAFLD male patients compared with male controls. In contrast, female NAFLD patients did not have significantly different miR levels compared with female controls. This pilot study showed empirical evidence for a male NAFLD-associated miR profile (Longchamps, et al., 2014). Again, some of these miRs, such as the hsa-miR-155, have been shown to play a role in inflammation. In addition to miR signatures, we also found a significantly elevated levels of the chemokine C-C motif ligand 16 (CCL-16) and the Vasoactive Intestinal Peptide (VIP) mRNA in IBS patients compared to controls. Within subsets of IBS patients, the CCL-16 gene expression was also upregulated in IBS-constipation patients, both compared to controls and IBS-diarrhea patients (Del Valle Pinero, et al., 2011). In light of the recent finding by others elucidating enhancement of CCL-16 protein function as a haptotactic gradient regulator for two key inflammatory cells, the monocytes and the lymphocytes, by matrix metalloproteases, our finding provides further evidence for a subclinical inflammatory mechanism in these patients. Likewise, the VIP gene expression from peripheral whole blood was significantly upregulated by 2.91-fold in IBS patients when compared to controls (Del Valle Pinero, et al., 2015). VIP is currently being looked at as a possible drug or therapeutic target for a number of GI disorders, because it is released in response to inflammation in the GI tract and suppresses the immune system causing a reduction in the inflammation. Finally, it is noteworthy that some of these miR and mRNA markers have been linked to gut epithelial barrier dynamics. Because of the increasingly recognized link between gut epithelial barrier dynamics and neurological function (Brain-Gut interactions), we also explored such link by examining the genetics of neuro-related behaviors, such as sleep, in our patients (Heitkemper, et al., 2015 and Reddy, et al., 2014). Laboratory experiments in cell and animal models designed to further explore these dynamics are in progress.